Difference between revisions of "CymR"
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− | * '''Description:''' pleiotropic regulator of | + | * '''Description:''' pleiotropic regulator of [[sulfur metabolism]] <br/><br/> |
{| align="right" border="1" cellpadding="2" | {| align="right" border="1" cellpadding="2" | ||
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|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor | |style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor | ||
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Function''' || regulation of | + | |style="background:#ABCDEF;" align="center"|'''Function''' || regulation of [[sulfur metabolism]] |
|- | |- | ||
− | |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/ | + | |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU27520 cymR] |
+ | |- | ||
+ | |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CymR CymR] | ||
+ | |- | ||
+ | |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=cymR cymR]''' | ||
|- | |- | ||
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 9.879 | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 11 kDa, 9.879 | ||
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrvO]]'', ''[[yrvN]]'' | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrvO]]'', ''[[yrvN]]'' | ||
|- | |- | ||
− | | | + | |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU27520 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU27520 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU27520 DNA_with_flanks] |
|- | |- | ||
|colspan="2" | '''Genetic context''' <br/> [[Image:yrzC_context.gif]] | |colspan="2" | '''Genetic context''' <br/> [[Image:yrzC_context.gif]] | ||
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div> | <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div> | ||
+ | |- | ||
+ | |colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cymR_2811717_2812133_-1 Expression at a glance]'''   {{PubMed|22383849}}<br/>[[Image:cymR_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU27520]] | ||
|- | |- | ||
|} | |} | ||
__TOC__ | __TOC__ | ||
+ | <br/><br/><br/><br/> | ||
+ | <br/><br/><br/><br/> | ||
+ | <br/><br/><br/><br/> | ||
+ | <br/><br/><br/><br/> | ||
+ | <br/><br/><br/><br/> | ||
+ | |||
− | + | <br/><br/><br/><br/><br/> | |
+ | = [[Categories]] containing this gene/protein = | ||
+ | {{SubtiWiki category|[[sulfur metabolism]]}}, | ||
+ | {{SubtiWiki category|[[transcription factors and their control]]}}, | ||
+ | {{SubtiWiki category|[[regulators of core metabolism]]}} | ||
+ | |||
+ | = This gene is a member of the following [[regulons]] = | ||
+ | {{SubtiWiki regulon|[[stringent response]]}} | ||
+ | =The [[CymR regulon]]= | ||
=The gene= | =The gene= | ||
Line 40: | Line 60: | ||
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
+ | * impaired growth in the presence of cystine and increased sensitivity to hydrogen peroxide-, disulfide-, paraquat- and tellurite-induced stresses {{PubMed|20608979}} | ||
+ | * increased intracellular cysteine pool and hydrogen sulfide formation {{PubMed|20608979}} | ||
+ | * depletion of branched-chain amino acids {{PubMed|20608979}} | ||
=== Database entries === | === Database entries === | ||
+ | * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU27520&redirect=T BSU27520] | ||
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cymR-yrvO-trmU.html] | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cymR-yrvO-trmU.html] | ||
Line 59: | Line 83: | ||
* '''Paralogous protein(s):''' | * '''Paralogous protein(s):''' | ||
+ | |||
+ | === Genes repressed by CymR === | ||
+ | * ''[[ytmI]]-[[tcyJ]]-[[tcyK]]-[[tcyL]]-[[tcyM]]-[[tcyN]]-[[ytmO]]-[[ytnI]]-[[ytnJ]]-[[ribR]]-[[ytnL]]-[[ytnM]]'' {{PubMed|16109943}} | ||
=== Extended information on the protein === | === Extended information on the protein === | ||
Line 72: | Line 99: | ||
* '''Effectors of protein activity:''' | * '''Effectors of protein activity:''' | ||
− | * '''Interactions:''' [[CymR]]-[[CysK]], the complex is formed in the presence of cysteine, and results in DNA binding and repression of genes of cysteine biosynthesis [http://www.ncbi.nlm.nih.gov/sites/entrez/18974048 PubMed] | + | * '''[[SubtInteract|Interactions]]:''' |
+ | ** [[CymR]]-[[CysK]], the complex is formed in the presence of cysteine, and results in DNA binding and repression of genes of cysteine biosynthesis [http://www.ncbi.nlm.nih.gov/sites/entrez/18974048 PubMed] | ||
− | * '''Localization:''' cytoplasm (according to Swiss-Prot) | + | * '''[[Localization]]:''' cytoplasm (according to Swiss-Prot) |
=== Database entries === | === Database entries === | ||
+ | * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU27520&redirect=T BSU27520] | ||
− | * '''Structure:''' | + | * '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=2Y75 2Y75] {{PubMed|21624051}} |
* '''UniProt:''' [http://www.uniprot.org/uniprot/O34527 O34527] | * '''UniProt:''' [http://www.uniprot.org/uniprot/O34527 O34527] | ||
Line 89: | Line 118: | ||
=Expression and regulation= | =Expression and regulation= | ||
+ | * '''Operon:''' ''[[cymR]]-[[yrvO]]-[[trmU]]'' {{PubMed|16885442}} | ||
− | * ''' | + | * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cymR_2811717_2812133_-1 cymR] {{PubMed|22383849}} |
− | * ''' | + | * '''Sigma factor:''' [[SigA]] {{PubMed|16885442}} |
* '''Regulation:''' | * '''Regulation:''' | ||
+ | ** [[RelA]] dependent downregulation (Class I) during stringent response {{PubMed|11948165}} | ||
* '''Regulatory mechanism:''' | * '''Regulatory mechanism:''' | ||
* '''Additional information:''' | * '''Additional information:''' | ||
+ | ** number of protein molecules per cell (minimal medium with glucose and ammonium): 508 {{PubMed|24696501}} | ||
+ | ** number of protein molecules per cell (complex medium with amino acids, without glucose): 1039 {{PubMed|24696501}} | ||
=Biological materials = | =Biological materials = | ||
Line 121: | Line 154: | ||
=References= | =References= | ||
+ | ==The [[CymR regulon]]== | ||
+ | <pubmed>16513748, </pubmed> | ||
+ | ==Other original publications== | ||
+ | <pubmed>18974048,17056751,16109943,16885442 11948165 , 15668000 20608979 21624051</pubmed> | ||
− | + | [[Category:Protein-coding genes]] |
Latest revision as of 09:35, 17 April 2014
- Description: pleiotropic regulator of sulfur metabolism
Gene name | cymR |
Synonyms | yrzC |
Essential | no |
Product | transcription repressor |
Function | regulation of sulfur metabolism |
Gene expression levels in SubtiExpress: cymR | |
Interactions involving this protein in SubtInteract: CymR | |
Metabolic function and regulation of this protein in SubtiPathways: cymR | |
MW, pI | 11 kDa, 9.879 |
Gene length, protein length | 333 bp, 111 aa |
Immediate neighbours | yrvO, yrvN |
Sequences | Protein DNA DNA_with_flanks |
Genetic context This image was kindly provided by SubtiList
| |
Expression at a glance PubMed |
Contents
Categories containing this gene/protein
sulfur metabolism, transcription factors and their control, regulators of core metabolism
This gene is a member of the following regulons
The CymR regulon
The gene
Basic information
- Locus tag: BSU27520
Phenotypes of a mutant
- impaired growth in the presence of cystine and increased sensitivity to hydrogen peroxide-, disulfide-, paraquat- and tellurite-induced stresses PubMed
- increased intracellular cysteine pool and hydrogen sulfide formation PubMed
- depletion of branched-chain amino acids PubMed
Database entries
- BsubCyc: BSU27520
- DBTBS entry: [1]
- SubtiList entry: [2]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity:
- Protein family: Rrf2 family of transcription regulators
- Paralogous protein(s):
Genes repressed by CymR
Extended information on the protein
- Kinetic information:
- Domains:
- Modification:
- Effectors of protein activity:
- Localization: cytoplasm (according to Swiss-Prot)
Database entries
- BsubCyc: BSU27520
- UniProt: O34527
- KEGG entry: [3]
- E.C. number:
Additional information
Expression and regulation
- Regulatory mechanism:
- Additional information:
Biological materials
- Mutant:
- Expression vector:
- lacZ fusion:
- GFP fusion:
- two-hybrid system:
- Antibody:
Labs working on this gene/protein
Isabelle Martin-Verstraete, Institute Pasteur, Paris, France
Your additional remarks
References
The CymR regulon
Sergine Even, Pierre Burguière, Sandrine Auger, Olga Soutourina, Antoine Danchin, Isabelle Martin-Verstraete
Global control of cysteine metabolism by CymR in Bacillus subtilis.
J Bacteriol: 2006, 188(6);2184-97
[PubMed:16513748]
[WorldCat.org]
[DOI]
(P p)
Other original publications
William Shepard, Olga Soutourina, Emmanuelle Courtois, Patrick England, Ahmed Haouz, Isabelle Martin-Verstraete
Insights into the Rrf2 repressor family--the structure of CymR, the global cysteine regulator of Bacillus subtilis.
FEBS J: 2011, 278(15);2689-701
[PubMed:21624051]
[WorldCat.org]
[DOI]
(I p)
Marie-Françoise Hullo, Isabelle Martin-Verstraete, Olga Soutourina
Complex phenotypes of a mutant inactivated for CymR, the global regulator of cysteine metabolism in Bacillus subtilis.
FEMS Microbiol Lett: 2010, 309(2);201-7
[PubMed:20608979]
[WorldCat.org]
[DOI]
(I p)
Catherine Tanous, Olga Soutourina, Bertrand Raynal, Marie-Françoise Hullo, Peggy Mervelet, Anne-Marie Gilles, Philippe Noirot, Antoine Danchin, Patrick England, Isabelle Martin-Verstraete
The CymR regulator in complex with the enzyme CysK controls cysteine metabolism in Bacillus subtilis.
J Biol Chem: 2008, 283(51);35551-60
[PubMed:18974048]
[WorldCat.org]
[DOI]
(P p)
Marie-Françoise Hullo, Sandrine Auger, Olga Soutourina, Octavian Barzu, Mireille Yvon, Antoine Danchin, Isabelle Martin-Verstraete
Conversion of methionine to cysteine in Bacillus subtilis and its regulation.
J Bacteriol: 2007, 189(1);187-97
[PubMed:17056751]
[WorldCat.org]
[DOI]
(P p)
Soon-Yong Choi, Dindo Reyes, Montira Leelakriangsak, Peter Zuber
The global regulator Spx functions in the control of organosulfur metabolism in Bacillus subtilis.
J Bacteriol: 2006, 188(16);5741-51
[PubMed:16885442]
[WorldCat.org]
[DOI]
(P p)
Pierre Burguière, Juliette Fert, Isabelle Guillouard, Sandrine Auger, Antoine Danchin, Isabelle Martin-Verstraete
Regulation of the Bacillus subtilis ytmI operon, involved in sulfur metabolism.
J Bacteriol: 2005, 187(17);6019-30
[PubMed:16109943]
[WorldCat.org]
[DOI]
(P p)
Irina M Solovieva, Rimma A Kreneva, Lubov Errais Lopes, Daniel A Perumov
The riboflavin kinase encoding gene ribR of Bacillus subtilis is a part of a 10 kb operon, which is negatively regulated by the yrzC gene product.
FEMS Microbiol Lett: 2005, 243(1);51-8
[PubMed:15668000]
[WorldCat.org]
[DOI]
(P p)
Christine Eymann, Georg Homuth, Christian Scharf, Michael Hecker
Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis.
J Bacteriol: 2002, 184(9);2500-20
[PubMed:11948165]
[WorldCat.org]
[DOI]
(P p)